SNPs Not just clustered in CODING regions. (interSNP distances typically LESS than 10kb)

Amount of sharing of SNPs between European Ancestry (Utah), Yoruba African Tribe, Chinese and Japanese population are similar BUT Chinese and Japanese have CLOSE relationship to each other compared to others

3. Detect sites on microarray where sample has hybridized using FLUORESCENT probe

Microarray chip details:

sequences printed on glass wafers.

Protective groups removed through light deprotection (only area where specific nucleotide, ie T, will be attached), then nucleotides (ie T) add onto linker molecule, and process repeats until about 25 nucleotides have attached to each sequence

25 nucleotides gives best specificity results

Phosphate groups present to prevent branching between sequences, but removed at final step

When any unprotected nucleotides are left after nucleotide addition step, they are CAPPED to prevent mutant sequences

Fluorescence from the sequences indicate binding has occurred to the feature

In the Styrkarsdottir et al paper the p-value they used to indicate statistical significance at the genome level was p = 1.7 x 10-7. Why did they set their p-value for significance so low? Why didnt they use the p = 0.05 value that is commonly used in statistics?

The significance was set so low because the study was testing for an association between 301,019 SNPs and the bone mineral density of the hip and lumbar spine. All these 300,000+ SNPs, in order to be reported as statistically significant, needed to be accounted for in order to get the genomic wide significance. The p-value was then taken as 0.05 (standardly used p-value in stats) DIVIDED by 301,019 SNPs in order to give this genomic wide significance.

****What is one of the major limitations of the HapMap data? To put that another way, now that research groups are beginning to use the HapMap data to look for genes associated with complex diseases or traits, what is one of the issues that they have encountered?

For some experiments, such as in the bone mineral density and fractures article, the sample sets included do not represent the entire species, but only subsets of the population.

They also discovered that the contribution of each allele may be very small in relation to correlating it to bone mineral density.

There may be a vast more amount of genes or loci tht may have SNPs that will also indicate a correlation, but have not been studied yet.

What are the functions of the different types of RNA polymerase in eukaryotic cells?

What are enhancers and silencers and how do they differ from the common promoter elements? Why can enhancers and silencers can be located 1000s of bps away from the genes they regulate?

Enhancers and repressors bind to proteins (transcription factors) to initiate or repress transcription.

Enhancers and silencers are sequences that are located within the promoter region (may also be 1000s of bps from start of transcription, in which case they can utilize DNA looping so the TFs that they are bound to can interact w/pol II and other TFs at start site of transcription.

An enhancer can also interact as a repressor for a different gene than it acts as an enhancer for.

Some enhancers may be involved with TFs that are needed to dimerize to function, and are done through an extensive regulatory complex through various developmental/environmental signals